Modeling

library(factoextra)

package ‘factoextra’ was built under R version 3.6.2Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa

#path to protected dbGap data location
local_path <- "~/Documents/MOMS-PI"# change me
#local_path <- "~/MOMS-PI"# change me
path2 <- file.path(local_path,"71694", "PhenoGenotypeFiles", "RootStudyConsentSet_phs001523.MOMS_PI.v1.p1.c1.DS-PREG-COM-IRB-PUB-MDS", "PhenotypeFiles") 
otu <- read.csv(file = file.path(path2, "MergedFiles", "OTU_table.csv"))
rownames(otu) <- otu$X
otu$X <- NULL 
t_otu <- as.data.frame(t(otu))
meta <- read.csv(file = file.path(path2, "MergedFiles", "Meta_data.csv"))
#physical activity variable
phys <- meta[,98:100]
meta$phys <- ifelse(meta$physical_activity_vigorous == "0_times" | is.na(meta$physical_activity_vigorous), "None", "Vigorous")
meta$phys[which(meta$phys == "None" & meta$physical_activity_moderate != "0_times" & !is.na(meta$physical_activity_moderate))] <- "Moderate"
meta$phys[which(meta$phys == "None" & meta$physical_activity_light != "0_times" & !is.na(meta$physical_activity_light))] <- "Light"
meta$phys <- as.factor(meta$phys)
#filter to just two races
meta <- meta %>%
  filter(race == "african_american" | race == "caucasian")
meta$race <- factor(meta$race)
rownames(meta) <- meta$X
meta$X <- NULL
t_otu <- t_otu[rownames(meta),]

meta <- meta %>%
  mutate(antibiotics_current = replace_na(antibiotics_current, "No"))
meta <- meta %>%
  mutate(infertility_treatment = replace_na(infertility_treatment, "No")) %>%
  mutate(infertility_treatment = recode(infertility_treatment, Not_sure = "No", .default = levels(meta$infertility_treatment)))
meta <- meta %>%
  mutate(vdischarge = replace_na(vdischarge, "No")) %>%
  mutate(vdischarge = recode(vdischarge, Not_Sure = "No", .default = levels(meta$vdischarge)))
meta <- meta %>%
  mutate(vodor = replace_na(vodor, "No")) %>%
  mutate(vodor = recode(vodor, Not_Sure = "No", .default = levels(meta$vodor)))
meta <- meta %>%
  mutate(vitching = replace_na(vitching, "No"))
meta <- meta %>%
  mutate(douche = replace_na(douche, "More_than_1_year_ago_or_never"))
meta <- meta %>%
  mutate(bv_history = replace_na(bv_history, "No")) %>%
  mutate(bv_history = recode(bv_history, Not_Sure = "No", .default = levels(meta$bv_history)))
meta <- meta %>%
  mutate(vaginitis_history = replace_na(vaginitis_history, "No"))
meta <- meta %>%
  mutate(current_medications = replace_na(current_medications, "No")) %>%
  mutate(current_medications = recode(current_medications, No_I_am_not_taking_any_new_medications = "No", .default = levels(meta$current_medications)))
meta <- meta %>%
  mutate(smoker_current = replace_na(smoker_current, "No"))
meta <- meta %>%
  mutate(alcohol_frequency_year = replace_na(alcohol_frequency_year, "0_times"))
meta <- meta %>%
  mutate(diabetes = replace_na(diabetes, "No")) %>%
  mutate(diabetes = recode(diabetes, Not_sure = "No", .default = levels(meta$diabetes)))
meta <- meta %>%
  mutate(no_false_labor = replace_na(no_false_labor, "Yes")) %>%
  mutate(no_false_labor = recode(no_false_labor, No_I_have_not_experienced_false_labor = "Yes", .default = levels(meta$no_false_labor)))
meta <- meta %>%
  mutate(no_high_bp = replace_na(no_high_bp, "Yes"))
meta <- meta %>%
  mutate(no_vbleeding = replace_na(no_vbleeding, "Yes"))
meta <- meta %>%
  mutate(progesterone = replace_na(progesterone, "No")) %>%
  mutate(progesterone = recode(progesterone, Not_Sure = "No", .default = levels(meta$progesterone)))
levels(meta$age)[1] <- NA

#Create combined table
full_set <- cbind(t_otu, meta)
full_set$alpha_div <- diversity(full_set[,1:length(names(t_otu))], index="shannon")
full_set$num_reads <- rowSums(t_otu)
#Add vagitype
mypropdata <- full_set[,colnames(t_otu)]
mytypes <- apply(mypropdata,1,which.max)
maxprop <- as.numeric(mypropdata[matrix(c(1:nrow(mypropdata),mytypes), ncol=2)])
mytypes <- colnames(mypropdata)[mytypes]
mytypes[maxprop < 0.3] <- "No Type"
mytypes <- as.factor(mytypes)
full_set <- full_set %>%
  mutate(vagitype=mytypes)
high_vagitype <- sort(table(full_set$vagitype), decreasing=T)[1:5]
high_vagitype

            Lactobacillus_iners Lactobacillus_crispatus_cluster           Lachnospiraceae_BVAB1 
                            714                             396                             228 
          Gardnerella_vaginalis   Lactobacillus_gasseri_cluster 
                            128                              64 

#Add proportions
full_set$p_Iners <- full_set$Lactobacillus_iners/full_set$num_reads
full_set$p_Crisp <- full_set$Lactobacillus_crispatus_cluster/full_set$num_reads
full_set$p_Gard <- full_set$Gardnerella_vaginalis/full_set$num_reads
full_set$Gass <- full_set$Lactobacillus_gasseri_cluster/full_set$num_reads
full_set$p_BVAB <- full_set$Lachnospiraceae_BVAB1/full_set$num_reads

get_mode = function(x, multimodal.na="TRUE"){
  modes <- Mode(x)
  if (multimodal.na=="FALSE" | length(modes)==1) {
    return(modes[1]) 
  } else {
    return(modes[length(modes)+1])
  }
}
#582 subjects
#aggregate at patient level
demog <- aggregate(visit_number ~ SUBJECT_ID, data = meta%>%data.frame, FUN = min)
demog <- merge(demog,meta%>%data.frame, by = c("SUBJECT_ID", "visit_number") )
  
#number visits per subject 
df <- aggregate(visit_number ~ SUBJECT_ID, data = meta%>%data.frame, FUN = length)
colnames(df)[which(colnames(df) == "visit_number")] <- "number of visits"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average income per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(income = get_mode(income, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "income")] <- "average income"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average education per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(education = get_mode(education, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "education")] <- "average education"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average age per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(age = get_mode(age, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "age")] <- "average age"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average prenatal care start per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(prenatal_care_start = get_mode(prenatal_care_start, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "prenatal_care_start")] <- "average p_care_start"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average infertility treatment per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(infertility_treatment = get_mode(infertility_treatment, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "infertility_treatment")] <- "average inf_trt"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average v_discharge per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(vdischarge = get_mode(vdischarge, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "vdischarge")] <- "average v_discharge"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average v_odor per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(vodor = get_mode(vodor, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "vodor")] <- "average v_odor"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average v_itching per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(vitching = get_mode(vitching, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "vitching")] <- "average v_itching"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average douche per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(douche = get_mode(douche, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "douche")] <- "average douche"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average bv_history per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(bv_history = get_mode(bv_history, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "bv_history")] <- "average bv_history"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average vaginitis_history per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(vaginitis_history = get_mode(vaginitis_history, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "vaginitis_history")] <- "average vaginitis_history"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average current_medications per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(current_medications = get_mode(current_medications, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "current_medications")] <- "average current_medications"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average smoker_current per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(smoker_current = get_mode(smoker_current, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "smoker_current")] <- "average smoker_current"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average alcohol_frequency per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(alcohol_frequency_year = get_mode(alcohol_frequency_year, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "alcohol_frequency_year")] <- "average alcohol_frequency"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average diabetes per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(diabetes = get_mode(diabetes, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "diabetes")] <- "average diabetes"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average false_labor per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(no_false_labor = get_mode(no_false_labor, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "no_false_labor")] <- "average no_false_labor"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average high_bp per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(no_high_bp = get_mode(no_high_bp, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "no_high_bp")] <- "average no_high_bp"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average v_bleeding per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(no_vbleeding = get_mode(no_vbleeding, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "no_vbleeding")] <- "average no_vbleeding"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average progesterone per subject 
df <- meta %>% group_by(SUBJECT_ID) %>% summarise(progesterone = get_mode(progesterone, multimodal.na = "FALSE"))
colnames(df)[which(colnames(df) == "progesterone")] <- "average progesterone"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#average vaginal_ph across visits
#Some patients have na so goes to 568
df <- aggregate(vaginal_pH ~ SUBJECT_ID, data = meta%>%data.frame, FUN = mean)
colnames(df)[which(colnames(df) == "vaginal_pH")] <- "mean_vaginal_ph"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#alpha diversity
df <- aggregate(alpha_div ~ SUBJECT_ID, data = full_set%>%data.frame, FUN = mean)
colnames(df)[which(colnames(df) == "alpha_div")] <- "mean_alpha_div"
demog <- merge(demog,df, by = c("SUBJECT_ID") )
#reported_ga is only for minimum recorded visit for each individual
Varnames <- c("mean_vaginal_ph", "number of visits", "reported_ga", "mean_alpha_div", "average income", 
              "average education", "average age", "average p_care_start", "average inf_trt", 
              "average  v_discharge", "average v_odor", "average v_itching", "average douche", 
              "average bv_history", "average vaginitis_history", "average current_medications",
              "average smoker_current", "average alcohol_frequency", "average diabetes", 
              "average no_false_labor", "average no_high_bp", "average no_vbleeding", "average progesterone")
#racial breakdown, break down visits and other demographics
stratified1 = tableone::CreateTableOne(
  vars = Varnames[1:4],
  data = summarytools::unlabel(demog), strata = "race", includeNA = TRUE)
stratified2 = tableone::CreateTableOne(
  vars = Varnames[5:7],
  data = summarytools::unlabel(demog), strata = "race", includeNA = TRUE)
stratified3 = tableone::CreateTableOne(
  vars = Varnames[8:15],
  data = summarytools::unlabel(demog), strata = "race", includeNA = TRUE)

The data frame does not have: average  v_discharge  Dropped

stratified4 = tableone::CreateTableOne(
  vars = Varnames[16:19],
  data = summarytools::unlabel(demog), strata = "race", includeNA = TRUE)
stratified5 = tableone::CreateTableOne(
  vars = Varnames[20:23],
  data = summarytools::unlabel(demog), strata = "race", includeNA = TRUE)

#stratified1 <- print(stratified1, printToggle = FALSE, showAllLevels = FALSE)
#stratified1 = stratified1[,!(colnames(stratified1) %in% "test")]%>%
#  knitr::kable(format="latex")%>% 
#  kable_styling("striped", full_width = F, font_size = 9)
stratified1

                              Stratified by race
                               african_american caucasian    p      test
  n                             366              152                    
  mean_vaginal_ph (mean (SD))  4.85 (0.80)      4.74 (0.72)   0.130     
  number of visits (mean (SD)) 3.57 (1.72)      3.36 (1.49)   0.196     
  reported_ga (%)                                             0.032     
     First Trimester             86 (23.5)        48 (31.6)             
     Second Trimester           179 (48.9)        76 (50.0)             
     Third Trimester             98 (26.8)        25 (16.4)             
     NA                           3 ( 0.8)         3 ( 2.0)             
  mean_alpha_div (mean (SD))   1.12 (0.59)      0.91 (0.65)  <0.001     

#fix the part where every race is shown, probably due to meta being called

#stratified1 <- print(stratified1, printToggle = FALSE, showAllLevels = FALSE)
#stratified1 = stratified1[,!(colnames(stratified1) %in% "test")]%>%
#  knitr::kable(format="latex")%>% 
#  kable_styling("striped", full_width = F, font_size = 9)
stratified2

                                    Stratified by race
                                     african_american caucasian   p      test
  n                                  366              152                    
  average income (%)                                              <0.001     
     15_000_19_999                    33 ( 9.0)         9 ( 5.9)             
     20_000_39_999                    40 (10.9)        20 (13.2)             
     40_000_59_999                     8 ( 2.2)        30 (19.7)             
     60_000_79_999                     3 ( 0.8)        25 (16.4)             
     80_000_or_more                    1 ( 0.3)        37 (24.3)             
     Under_15_000                    267 (73.0)        27 (17.8)             
     NA                               14 ( 3.8)         4 ( 2.6)             
  average education (%)                                           <0.001     
     2_year_College_Degree            29 ( 7.9)        16 (10.5)             
     4_year_College_Degree             7 ( 1.9)        47 (30.9)             
     Doctoral_or_Professional_Degree   1 ( 0.3)        18 (11.8)             
     High_School_GED                 182 (49.7)        27 (17.8)             
     Less_than_High_School            50 (13.7)         1 ( 0.7)             
     Masters_Degree                    2 ( 0.5)        19 (12.5)             
     Some_College                     91 (24.9)        24 (15.8)             
     NA                                4 ( 1.1)         0 ( 0.0)             
  average age (%)                                                 <0.001     
                                       0 ( 0.0)         1 ( 0.7)             
     18                                7 ( 1.9)         1 ( 0.7)             
     18_to_28                        239 (65.3)        49 (32.2)             
     29-38                            97 (26.5)        91 (59.9)             
     Above_38                         15 ( 4.1)         9 ( 5.9)             
     Below_18                          6 ( 1.6)         1 ( 0.7)             
     NA                                2 ( 0.5)         0 ( 0.0)             

#fix the part where every race is shown, probably due to meta being called

#stratified1 <- print(stratified1, printToggle = FALSE, showAllLevels = FALSE)
#stratified1 = stratified1[,!(colnames(stratified1) %in% "test")]%>%
#  knitr::kable(format="latex")%>% 
#  kable_styling("striped", full_width = F, font_size = 9)
stratified3

                                                          Stratified by race
                                                           african_american caucasian   p      test
  n                                                        366              152                    
  average p_care_start (%)                                                              <0.001     
     0_4_weeks_after_conception                            101 (27.6)        33 (21.7)             
     4_weeks_to_the_end_of_the_first_trimester             157 (42.9)        88 (57.9)             
     Before_conception                                       9 ( 2.5)        11 ( 7.2)             
     During_the_second_trimester                            51 (13.9)        14 ( 9.2)             
     During_the_third_trimester                              7 ( 1.9)         2 ( 1.3)             
     I_did_not_receive_prenatal_care                        15 ( 4.1)         0 ( 0.0)             
     I_have_not_yet_received_prenatal_care_but_planning_to  18 ( 4.9)         1 ( 0.7)             
     NA                                                      8 ( 2.2)         3 ( 2.0)             
  average inf_trt = Yes (%)                                  5 ( 1.4)        10 ( 6.6)   0.003     
  average v_odor = Yes (%)                                  30 ( 8.2)         4 ( 2.6)   0.033     
  average v_itching = Yes (%)                               23 ( 6.3)         5 ( 3.3)   0.246     
  average douche (%)                                                                    <0.001     
     More_than_1_month_ago                                  84 (23.0)         8 ( 5.3)             
     More_than_1_year_ago_or_never                         279 (76.2)       144 (94.7)             
     Within_the_last_24_hours                                3 ( 0.8)         0 ( 0.0)             
  average bv_history (%)                                                                 0.494     
     No                                                    286 (78.1)       125 (82.2)             
     Yes                                                    79 (21.6)        27 (17.8)             
     NA                                                      1 ( 0.3)         0 ( 0.0)             
  average vaginitis_history = Yes (%)                       13 ( 3.6)         2 ( 1.3)   0.274     

#fix the part where every race is shown, probably due to meta being called

#stratified1 <- print(stratified1, printToggle = FALSE, showAllLevels = FALSE)
#stratified1 = stratified1[,!(colnames(stratified1) %in% "test")]%>%
#  knitr::kable(format="latex")%>% 
#  kable_styling("striped", full_width = F, font_size = 9)
stratified4

                                       Stratified by race
                                        african_american caucasian   p      test
  n                                     366              152                    
  average current_medications = Yes (%) 141 (38.5)        99 (65.1)  <0.001     
  average smoker_current = Yes (%)       54 (14.8)        21 (13.8)   0.889     
  average alcohol_frequency (%)                                      <0.001     
     0_times                            223 (60.9)        36 (23.7)             
     1_2_times                           54 (14.8)        28 (18.4)             
     10_19_times                         12 ( 3.3)        20 (13.2)             
     20_times                            13 ( 3.6)        37 (24.3)             
     3_5_times                           42 (11.5)        19 (12.5)             
     6_9_times                           21 ( 5.7)        12 ( 7.9)             
     NA                                   1 ( 0.3)         0 ( 0.0)             
  average diabetes (%)                                                0.529     
     No                                 356 (97.3)       145 (95.4)             
     Yes                                  9 ( 2.5)         6 ( 3.9)             
     NA                                   1 ( 0.3)         1 ( 0.7)             

#fix the part where every race is shown, probably due to meta being called

#stratified1 <- print(stratified1, printToggle = FALSE, showAllLevels = FALSE)
#stratified1 = stratified1[,!(colnames(stratified1) %in% "test")]%>%
#  knitr::kable(format="latex")%>% 
#  kable_styling("striped", full_width = F, font_size = 9)
stratified5

                            Stratified by race
                             african_american caucasian   p      test
  n                          366              152                    
  average no_false_labor (%)                               NaN       
                               0 ( 0.0)         0 ( 0.0)             
     No                       37 (10.1)         2 ( 1.3)             
     Yes                     321 (87.7)       148 (97.4)             
     NA                        8 ( 2.2)         2 ( 1.3)             
  average no_high_bp (%)                                   NaN       
                               0 ( 0.0)         0 ( 0.0)             
     No                       42 (11.5)         9 ( 5.9)             
     Yes                     312 (85.2)       140 (92.1)             
     NA                       12 ( 3.3)         3 ( 2.0)             
  average no_vbleeding (%)                                 0.057     
                               0 ( 0.0)         3 ( 2.0)             
     No                       31 ( 8.5)        14 ( 9.2)             
     Yes                     327 (89.3)       131 (86.2)             
     NA                        8 ( 2.2)         4 ( 2.6)             
  average progesterone (%)                                 0.520     
     No                      358 (97.8)       147 (96.7)             
     Yes                       7 ( 1.9)         5 ( 3.3)             
     NA                        1 ( 0.3)         0 ( 0.0)             

#fix the part where every race is shown, probably due to meta being called

#Find out individuals who have a different vagitype across visits
uniq_vagitype <- full_set %>%
  group_by(SUBJECT_ID) %>%
  summarize(n_unique = n_distinct(vagitype))
more_vagitype <- uniq_vagitype %>%
  filter(n_unique > 1)
full_set %>%
  filter(SUBJECT_ID %in% more_vagitype$SUBJECT_ID) %>%
  group_by(SUBJECT_ID) %>%
  distinct(vagitype)

#Look at proportional changes over time, look at differences betweeen those that did change and those that did not
#Look at how they change, if they change similarly

count_table <- aggregate(list(full_set$Lactobacillus_iners, full_set$p_Iners,full_set$Lactobacillus_crispatus_cluster, full_set$p_Crisp, full_set$Gardnerella_vaginalis, full_set$p_Gard, full_set$Lactobacillus_gasseri_cluster, full_set$Gass, full_set$Lachnospiraceae_BVAB1, full_set$p_BVAB), by = list(full_set$race, full_set$reported_ga), mean)
colnames(count_table) <- c("race", "reported_ga", "Lactobacillus_iners", "p_Iners", "Crispatus", "p_Crisp", 
                           "Gardnerella", "p_Gard", "Gasseri", "p_Gass", "BVAB", "p_BVAB")
count_table <- count_table %>%
  arrange(race)
kable(count_table,  table.attr = "style = \"color: black;\"") %>%
  kable_styling(bootstrap_options = c("striped", "hover"))

race	reported_ga	Lactobacillus_iners	p_Iners	Crispatus	p_Crisp	Gardnerella	p_Gard	Gasseri	p_Gass	BVAB	p_BVAB
african_american	First Trimester	14505.96	0.2517823	8966.637	0.1340359	7985.951	0.1107511	652.6078	0.0149517	8863.471	0.1252649
african_american	Second Trimester	21640.13	0.3400013	10559.085	0.1383411	5455.281	0.0905662	867.7945	0.0155340	10614.083	0.1433958
african_american	Third Trimester	26061.41	0.4024149	10693.302	0.1511822	3437.836	0.0607404	1055.6137	0.0177334	7438.261	0.1027035
caucasian	First Trimester	12899.98	0.1803131	24551.900	0.3699975	9399.640	0.1066708	2068.4200	0.0527995	1095.420	0.0132448
caucasian	Second Trimester	12919.27	0.2402719	27804.674	0.3455106	3564.785	0.0595546	5281.7403	0.0920684	3087.961	0.0345624
caucasian	Third Trimester	14819.43	0.2555657	23575.302	0.3017310	3401.765	0.0562494	4193.1306	0.0713278	1420.843	0.0170265

#Plot proportions over time, plot count over time
iners <- ggplot(count_table, aes(reported_ga, p_Iners)) + 
  geom_line(aes(group=race, color=race)) 
crisp <- ggplot(count_table, aes(reported_ga, p_Crisp)) + 
  geom_line(aes(group=race, color=race)) 
gard <- ggplot(count_table, aes(reported_ga, p_Gard)) + 
  geom_line(aes(group=race, color=race)) 
gass <- ggplot(count_table, aes(reported_ga, p_Gass)) + 
  geom_line(aes(group=race, color=race)) 
bvab <- ggplot(count_table, aes(reported_ga, p_BVAB)) + 
  geom_line(aes(group=race, color=race)) 
library(gridExtra)

Attaching package: ‘gridExtra’

The following object is masked from ‘package:dplyr’:

    combine

ggarrange(iners, crisp, bvab, gard, gass, nrow = 3)

$`1`

$`2`

attr(,"class")
[1] "list"      "ggarrange"

#Plot individuals for each race
#ggplot(full_set, aes(reported_ga, p_Iners)) + 
#  geom_line(aes(group=SUBJECT_ID, color=race)) + 
#  facet_wrap(~race, ncol=1)
#Look at those with the specific taxa as their vagitype

prop_plot <- ggplot(full_set, aes(p_Iners)) + geom_histogram() + geom_vline(xintercept=mean(full_set$p_Iners), lwd=1, linetype=2, color="red") + geom_vline(xintercept=median(full_set$p_Iners), lwd=1, linetype=2, color="green")
#prop_plot
cprop_plot <- ggplot(full_set, aes(p_Crisp)) + geom_histogram() + geom_vline(xintercept=mean(full_set$p_Crisp), lwd=1, linetype=2, color="red") + geom_vline(xintercept=median(full_set$p_Crisp), lwd=1, linetype=2, color="green")
#iprop_plot
bprop_plot <- ggplot(full_set, aes(p_BVAB)) + geom_histogram() + geom_vline(xintercept=mean(full_set$p_BVAB), lwd=1, linetype=2, color="red") + geom_vline(xintercept=median(full_set$p_BVAB), lwd=1, linetype=2, color="green")
#pprop_plot
gprop_plot <- ggplot(full_set, aes(p_Gard)) + geom_histogram() + geom_vline(xintercept=mean(full_set$p_Gard), lwd=1, linetype=2, color="red") + geom_vline(xintercept=median(full_set$p_Gard), lwd=1, linetype=2, color="green")
#tprop_plot
gasprop_plot <- ggplot(full_set, aes(Gass)) + geom_histogram() + geom_vline(xintercept=mean(full_set$Gass), lwd=1, linetype=2, color="red") + geom_vline(xintercept=median(full_set$Gass), lwd=1, linetype=2, color="green")
#bprop_plot
#stratify by race
ggarrange(prop_plot, cprop_plot, bprop_plot, gprop_plot, gasprop_plot, labels = c("Iners","Crisp", "BVAB", "Gard", "Gass"), ncol = 3, nrow = 2)

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

race_prop_plot <- ggplot(full_set, aes(p_Iners)) + geom_histogram(aes(group=race, fill=race)) + facet_wrap(~race) 
crace_prop_plot <- ggplot(full_set, aes(p_Crisp)) + geom_histogram(aes(group=race, fill=race)) + facet_wrap(~race) 
#stratify by race
brace_prop_plot <- ggplot(full_set, aes(p_BVAB)) + geom_histogram(aes(group=race, fill=race)) + facet_wrap(~race) 
grace_prop_plot <- ggplot(full_set, aes(p_Gard)) + geom_histogram(aes(group=race, fill=race)) + facet_wrap(~race)
gassrace_prop_plot <- ggplot(full_set, aes(Gass)) + geom_histogram(aes(group=race, fill=race)) + facet_wrap(~race)
ggarrange(race_prop_plot, crace_prop_plot, brace_prop_plot, grace_prop_plot, gassrace_prop_plot, nrow = 3)

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

$`1`

$`2`

attr(,"class")
[1] "list"      "ggarrange"

#Zero-Inflated Poisson Model
z <- glmmTMB(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div + (1|SUBJECT_ID), data = full_set, family = poisson, zi = ~ vaginal_pH + reported_ga + alpha_div)
summary(z)
hist(predict(z))

#summary(m1 <- zeroinfl(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div |SUBJECT_ID, data = full_set))
z <- glmmTMB(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div + (1|SUBJECT_ID), data = full_set, family = poisson, zi = ~ 0)
summary(z)
hist(predict(z))


#Zero-Inflated Negative Binomial Model
neg_bin<- glmmTMB(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div + offset(log(num_reads)) + (1|SUBJECT_ID), data = full_set, family = nbinom2, zi = ~ vaginal_pH + reported_ga + alpha_div)
summary(neg_bin)
predict(neg_bin)
neg_binone <- glmmTMB(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div + offset(log(num_reads)) + (1|SUBJECT_ID), data = full_set, family = nbinom2, zi = ~ 1)
summary(neg_binone)
hist(predict(neg_binone))
#Zero-Inflated Beta-Binomial Model
#kostic.y <- cbind(1, kostic.y=="Tumor")
beta_bin<- glmmTMB(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div + race + (1|SUBJECT_ID), data = full_set, family=betabinomial(link = "logit"), zi = ~ vaginal_pH + reported_ga + alpha_div + race)


#Mixed Linear Regression Model
mixedL <- lmer(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div + race + (1|SUBJECT_ID), data = full_set)
summary(mixedL)
linpred <- predict(mixedL)
plot(full_set$Lactobacillus_iners[which(names(linpred) %in% rownames(full_set))], linpred)
#predicted
#x-axis people
#y-axis visits for that person
plot(full_set$Lactobacillus_iners[which(names(linpred) %in% rownames(full_set))], linpred)


## Beta bimonial zero inflated ##

## NBZIMM ##
f21 = glmm.zinb(Lactobacillus_iners ~ vaginal_pH + reported_ga + alpha_div , random = ~ 1|SUBJECT_ID, data = full_set)
summary(f21)
summary(f21)$tTable[4, 5]

hist(full_set$p_Iners)
beta_bin<- glmmTMB(p_Iners ~ vaginal_pH + reported_ga + alpha_div + race + (1|SUBJECT_ID), data = full_set, family=betabinomial(link = "logit"), zi = ~ vaginal_pH + reported_ga + alpha_div + race)
mean(full_set$p_Iners)
var(full_set$p_Iners)

library(zoib)
#zoib
#zoib(p_Iners ~ vaginal_pH + reported_ga + alpha_div + race | 1|1, data = full_set, random = 1, EUID = full_set$SUBJECT_ID)
library(aod)
full_set$p_Iners[which(full_set$p_Iners == 1)] <- 0.99999
betaIners <- glmmTMB(p_Iners ~ vaginal_pH + reported_ga + alpha_div + race + (1|SUBJECT_ID), data = full_set, family=beta_family(link = "logit"), zi = ~ 1)
betapred <- predict(betaIners)
summary(betaIners)
#predicted
#x-axis people
#y-axis visits for that person
#plot(full_set$p_Iners[which(names(betapred) %in% rownames(full_set))], betapred)

#zoib(p_Iners ~ vaginal_pH + reported_ga + alpha_div + race | 1, data = full_set)


mixedL <- lmer(p_Iners ~ vaginal_pH + reported_ga + alpha_div + race + (1|SUBJECT_ID), data = full_set)

#par(mfrow = c(2,2))

coefplot2(mixedL)
plot(mixedL)
linpred <- predict(mixedL)

#predicted
#x-axis people
#y-axis visits for that person
plot(full_set$p_Iners[which(names(linpred) %in% rownames(full_set))], linpred)

full_set$class_Iners <- as.factor(ifelse(full_set$p_Iners > mean(full_set$p_Iners), "High", "Low"))
full_set$class_Crisp <- as.factor(ifelse(full_set$p_Crisp > mean(full_set$p_Crisp), "High", "Low"))
full_set$class_Gass <- as.factor(ifelse(full_set$Gass > mean(full_set$Gass), "High", "Low"))
full_set$class_Gard <- as.factor(ifelse(full_set$p_Gard > mean(full_set$p_Gard), "High", "Low"))
full_set$class_BVAB <- as.factor(ifelse(full_set$p_BVAB > mean(full_set$p_BVAB), "High", "Low"))


#Check median
#add line to show where each point is

#install.packages("ggpubr")
iners_plot <- ggplot(full_set, aes(class_Iners)) + geom_bar()
snea_plot <- ggplot(full_set, aes(class_Crisp)) + geom_bar() 
tm_plot <- ggplot(full_set, aes(class_Gass)) + geom_bar() 
prev_plot <- ggplot(full_set, aes(class_Gard)) + geom_bar() 
bvab_plot <- ggplot(full_set, aes(class_BVAB)) + geom_bar()

ggarrange(iners_plot, snea_plot, tm_plot, prev_plot, bvab_plot, labels = c("Iners", "Crisp", "Gass", "Gard", "BVAB1"), ncol = 3, nrow = 2)

#Distribution of High and Low (do it across race)
irace_prop_plot <- ggplot(full_set, aes(class_Iners)) + geom_bar(aes(y= stat(prop),group=race, fill=race), position = "dodge2")+ ggtitle("Iners Dichotomized Histogram")
irace_prop_plot

#Distribution of High and Low (do it across race)
srace_prop_plot <- ggplot(full_set, aes(class_Crisp)) + geom_bar(aes(y= stat(prop), group=race, fill=race), position = "dodge2") + ggtitle("Crisp Dichotomized Histogram")
#Distribution of High and Low (do it across race)
prace_prop_plot <- ggplot(full_set, aes(class_Gass)) + geom_bar(aes(y= stat(prop), group=race, fill=race), position = "dodge2") +  ggtitle("Gass Dichotomized Histogram")
#Distribution of High and Low (do it across race)
trace_prop_plot <- ggplot(full_set, aes(class_Gard)) + geom_bar(aes(y= stat(prop), group=race, fill=race), position = "dodge2") + ggtitle("Gard Dichotomized Histogram")
#Distribution of High and Low (do it across race)
brace_prop_plot <- ggplot(full_set, aes(class_BVAB)) + geom_bar(aes(y= stat(prop),group=race, fill=race), position = "dodge2") + ggtitle("BVAB Dichotomized Histogram")
ggarrange(irace_prop_plot, srace_prop_plot, prace_prop_plot, trace_prop_plot, brace_prop_plot, nrow = 3)

$`1`

$`2`

attr(,"class")
[1] "list"      "ggarrange"

#Use proportions instead of counts for better comparison, DONE
#position dodge, DONE
#Add proportion values to top of bars
#do facet wrap by taxa

covs.taxa <- function(df, taxon, model, vars){
  tax_prop <- df[,taxon]/df[,"num_reads"]
   if(model == "fixed"){
    #covs <- vars
    model_data <- df[,vars]
    half <- paste(vars, collapse= "+")
  }
  else{
    #covs <- vars
    model_data <- df[,c(vars, "SUBJECT_ID", "num_reads")]
    half <- paste(paste(vars, collapse= "+"), " + (1|SUBJECT_ID)")
  }
  model_data <- cbind(tax_prop, model_data)
  no.na.data <- na.omit(model_data)
  form <- as.formula(paste("tax_prop ~ ", half))
  if(model == "fixed"){
    mod <- lm(form, data = no.na.data)
    step.back <- stepAIC(mod, direction = "backward")
    return(step.back)
    #return(mod)
  }
  else{
    mod <- lmer(form, data = no.na.data)
    return(mod)
    #return(mod.step)
  }
}

taxa.glm <- function(df, taxon, type, model){
  tax_count <- df[,taxon]
  tax_prop <- df[,taxon]/df[,"num_reads"]
  class_tax <- as.factor(ifelse(tax_prop > mean(tax_prop), "High", "Low"))
  class_tax <- recode(class_tax, "High"= 1, "Low"= 0)
  if(model == "fixed"){
    covs <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "income", "bv_history", "phys", "antibiotics_current","age", "education", "prenatal_care_start", "infertility_treatment", "vdischarge", "vodor", "vitching", "douche", "vaginitis_history", "current_medications", "smoker_current", "alcohol_frequency_year", "diabetes", "no_false_labor", "no_high_bp", "no_vbleeding", "progesterone")
    model_data <- df[,covs]
    half <- paste(covs, collapse= "+")
  }
  else{
    covs <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "income", "bv_history", "phys", "antibiotics_current","age", "education", "prenatal_care_start", "infertility_treatment", "vdischarge", "vodor", "vitching", "douche", "vaginitis_history", "current_medications", "smoker_current", "alcohol_frequency_year", "diabetes", "no_false_labor", "no_high_bp", "no_vbleeding", "progesterone")
    model_data <- df[,c(covs, "SUBJECT_ID", "num_reads")]
    half <- paste(paste(covs, collapse= "+"), " + (1|SUBJECT_ID)")
  }
  if(type == "count"){
    model_data <- cbind(tax_count, model_data)
    no.na.data <- na.omit(model_data)
    form <- as.formula(paste("tax_count ~ ", half))
    if(model == "fixed"){
      mod <- glm.nb(form, data = no.na.data)
    }
    else{
      mod <- glmer.nb(form, data = no.na.data)
    }
  }
  else if(type == "prop"){
    model_data <- cbind(tax_prop, model_data)
    no.na.data <- na.omit(model_data)
    form <- as.formula(paste("tax_prop ~ ", half))
    if(model == "fixed"){
      mod <- lm(form, data = no.na.data)
      #return(mod)
    }
    else{
      mod <- lmer(form, data = no.na.data)
      return(mod)
      #return(mod.step)
    }
  }
  else{
    model_data <- cbind(class_tax, model_data)
    no.na.data <- na.omit(model_data)
    form <- as.formula(paste("class_tax ~ ", paste(covs, collapse= "+")))
    if(model == "fixed"){
      mod <- glm(form, data = no.na.data, family = binomial)
    }
    else{
      mod <- glmer(form, data = no.na.data, family = binomial, control=glmerControl(optimizer="bobyqa",optCtrl=list(maxfun=2e5)))
    }
  }
  #step.model <- stepAIC(fixed_mod, direction = "both", trace = FALSE)
  step.back <- stepAIC(mod, direction = "backward", trace = FALSE)
  return(step.back)
  #TO ADD: Plot for each covariate the predicted distribution
  #Output table of common variables, extract p-value
}

model_plot <- function(model){
  final_covs <- names(model$model)[-1]
  print(deparse(substitute(model)))
  print(as.formula(paste("class_tax ~ ", paste(final_covs, collapse= "+"))))
  #Plot AIC for model
  vars <- unlist(lapply(strsplit(as.character(model$anova$Step), '- ', fixed = TRUE), '[', 2))
  vars[1] <- "Intercept"
  AIC.res <- data.frame(Variable = vars, AIC = model$anova$AIC)
  AIC.res$Variable <- factor(AIC.res$Variable, levels = vars)
  #true variables
  #true_vars <- paste0("var", 1:10)
  #colour_vars <- ifelse(AIC.res$Variable %in% true_vars, 'red','black')
  plot <- ggplot(data=AIC.res, aes(x=Variable, y=AIC, group=1)) +
    geom_line(color = "red")+
    theme_bw()+
    theme(axis.text.x = element_text(angle = 60, hjust = 1))
  return(plot)
}

pred_plot <- function(df, model){
  model_data <- df[,covs]
  model_data <- cbind(class_tax, model_data)
  no.na.data <- na.omit(model_data)
  final_covs <- names(model$model)[-1]
  pred_data <- no.na.data[,final_covs]
  return(predict(model, newdata=pred_data, type = "response"))
  
  
  
  # if(c("alpha_div","vagitype") %in% names(model$model)){
  #   plotting_dfm <- expand.grid(alpha_div = seq(0, 3.5, 0.01),
  #                          vagitype = c("Lactobacillus_crispatus_cluster", "Lactobacillus_iners", "Lachnospiraceae_BVAB1", "Gardnerella_vaginalis", "Lactobacillus_gasseri_cluster"))
  #   plotting_dfm$preds <- predict(model, newdata=plotting_dfm, type = "response")
  #   pl <- ggplot(plotting_dfm, aes(x=alpha_div, y =preds, color=as.factor(vagitype))) +
  #     geom_point( ) +
  #     ggtitle("Predicted High/Low by Alpha_Div and Vagitype")
  #   return(p1)
  # }
  # else{
  #   return ("No value")
  # }
}

get_data <- function(taxon, df){
  tax_prop <- df[,taxon]/df[,"num_reads"]
  covs <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "income", "bv_history", "phys", "antibiotics_current","age", "education", "prenatal_care_start", "infertility_treatment", "vdischarge", "vodor", "vitching", "douche", "vaginitis_history", "current_medications", "smoker_current", "alcohol_frequency_year", "diabetes", "no_false_labor", "no_high_bp", "no_vbleeding", "progesterone")
  model_data <- df[,c(covs, "SUBJECT_ID", "num_reads")]
  model_data <- cbind(tax_prop, model_data)
  no.na.data <- na.omit(model_data)
  return(no.na.data)
}

make_hists<- function(model, taxon, df, vars){
  hists <- data.frame(xx = c(predict(model, newdata = get_data(taxon, df)[, vars]), get_data(taxon, df)[, "tax_prop"]), yy = rep(c("pred", "actual"),each = length(get_data(taxon, df)[, "tax_prop"])))
  return(ggplot(hists, aes(x=xx, fill=yy)) + geom_histogram(alpha=0.2, position="identity"))
}

agg_plot <- function(model, taxon, df, vars){
  ex <- data.frame(data = c(predict(model, newdata = get_data(taxon, df)[, vars]), get_data(taxon, df)[, "tax_prop"]), 
                   race = get_data(taxon, df)[, "race"], tri = get_data(taxon, df)[, "reported_ga"],
                   yy = rep(c("pred", "actual"),each = length(get_data(taxon, df)[, "tax_prop"])))
  agg_table <- aggregate(list(ex$data), by = list(ex$race, ex$tri, ex$yy), mean)
  colnames(agg_table) <- c("race", "tri", "type", "data")
  agg_plot <- ggplot(agg_table, aes(tri, data)) + 
geom_line(aes(group=interaction(race, type), color=race, linetype = type)) + 
    scale_x_discrete(labels=c("First Trimester" = "1st", "Second Trimester" = "2nd",
                              "Third Trimester" = "3rd")) + 
    ylab("Prop")
  return(agg_plot)
}

getPerformace <- function(model, df){
  taxa <- colnames(t_otu)
  example <- c("Lactobacillus_iners", "Lactobacillus_crispatus_cluster", "Gardnerella_vaginalis", "Lachnospiraceae_BVAB1", "Lactobacillus_gasseri_cluster", "Sneathia_amnii", "Prevotella_cluster2", "TM7_OTU-H1")
  for (name in example){
    md <- covs.taxa
  }
  perf <- model_performance(model, metrics = "all", verbose = TRUE)
  return(perf)
  
}

subsetFull <- function(df, taxalist){
  `%ni%` <- Negate(`%in%`)
  cols <- sapply(taxalist, function (x) any(df[,x]/df$num_reads > 0.05))
  df <- subset(df,select = names(df) %ni% names(which(cols == FALSE)))
  return(df)
}
  

covs <- c("vaginal_pH", "alpha_div", "reported_ga", "race", "income", "bv_history", "phys", "antibiotics_current","age", "education", "prenatal_care_start", "infertility_treatment", "vdischarge", "vodor", "vitching", "douche", "vaginitis_history", "current_medications", "smoker_current", "alcohol_frequency_year", "diabetes", "no_false_labor", "no_high_bp", "no_vbleeding", "progesterone")
model_data <- full_set[,covs]
ggpairs(model_data, columns = 1:2, ggplot2::aes(colour=race)) #too many points, too many vagitypes as well so had to remove
#do top 5 vagitypes
aa <- full_set[full_set$race == 'african_american',]
histogram(aa$vaginal_pH)

count_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "count", "fixed") #Does not converge
prop_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "prop", "fixed")
class_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "class", "fixed")
mcount_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "count", "mixed") #Does not converge
mprop_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "prop", "mixed") #failure to converge in 10000 evaluations
mod_Crisp <- taxa.glm(full_set, "Lactobacillus_crispatus_cluster", "class", "fixed")
mod_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "class", "fixed")
mod_BVAB <- taxa.glm(full_set, "Lachnospiraceae_BVAB1", "class", "fixed")
mod_Gard <- taxa.glm(full_set, "Gardnerella_vaginalis", "class", "fixed")
mod_Gass <- taxa.glm(full_set, "Lactobacillus_gasseri_cluster", "class", "fixed")


taxalist <- c("Lactobacillus_crispatus_cluster", "Lactobacillus_iners", "Lachnospiraceae_BVAB1", "Gardnerella_vaginalis", "Lactobacillus_gasseri_cluster")
var_df <- data.frame(matrix(ncol = 15, nrow = 15))
#colnames(var_df) <- taxalist
count <- 0
for(ind in c(1:length(taxalist))){
  mods <- taxa.glm(full_set, taxalist[ind], "prop", "mixed")
  no.na.data <- get_data(taxalist[ind], full_set)
  step.back <- lmerTest::step(mods)
  fix_vars <- c(rownames(step.back$fixed[which(step.back$fixed$Eliminated == 0),]), rownames(step.back$random[which(step.back$random$Eliminated == 0),]))
  for(i in c(1:length(fix_vars))){
    var_df[i,ind+count] <- fix_vars[i]
  }
  fixed_mods <- taxa.glm(full_set, taxalist[ind], "prop", "fixed")
  fixed_vars <- names(fixed_mods$model)[-1]
  for(i in c(1:length(fixed_vars))){
    var_df[i,ind+1+count] <- fixed_vars[i]
  }
  class_mods <- taxa.glm(full_set, taxalist[ind], "class", "fixed")
  class_vars <- names(class_mods$model)[-1]
  for(i in c(1:length(class_vars))){
    var_df[i,ind+2+count] <- class_vars[i]
  }
  count <- count + 2
}

colnames(var_df) <- c("Crisp_P_M", "Crisp_P_F", "Crisp_C_F", "Iners_P_M", "Iners_P_F","Iners_C_F", "BVAB1_P_M", "BVAB1_P_F","BVAB1_C_F","Gard_P_M", "Gard_P_F", "Gard_C_F","Gass_P_M","Gass_P_F", "Gass_C_F")
options(knitr.kable.NA = '')
kable(var_df, table.attr = "style = \"color: black;\"") %>%
  kable_styling(bootstrap_options = c("striped", "hover")) %>%
  add_header_above(c("Crispatus" = 3, "Iners" = 3, "BVAB" = 3, "Gardnerella" = 3, "Gasseri" = 3))

#Make table for the variables that are outputted
#need the data frame
#alpha div, vagitype, age, smoking, education, subject_id, vaginal_ph, race
#look at covariate estimates for each taxa model, consider correlations in model
#forward model selection, one variable addition at a time
#look at differences between taxa
#look for vagitypes in rare taxa
#performance with and without vagitype, compare using model comparison,ANOVA DONE
#overlay averages across each race across the 3 trimesters, output model metrics, try without and with vagitype: WROTE FUNCTION, APPLY TO ALL TAXA
#how much does vagitype add in terms of prediction, PLOTS DONE
#make summaries
#pca under both smoothed and unsmoother conditions
#prcomp on raw data, scale variables to same unit

vars <- c("vaginal_pH", "alpha_div", "race", "vagitype", "age", "education", "smoker_current")
mx_vars<- c("vaginal_pH", "alpha_div", "race", "vagitype", "age", "education", "smoker_current", "reported_ga","SUBJECT_ID")
mx_type <- c("vaginal_pH", "alpha_div", "race", "age", "education", "smoker_current", "reported_ga","SUBJECT_ID")
no_type <- c("vaginal_pH", "alpha_div", "race", "age", "education", "smoker_current")

#predict based on these models

taxalist <- c("Lactobacillus_iners", "Lactobacillus_crispatus_cluster", "Gardnerella_vaginalis", "Lachnospiraceae_BVAB1", "Lactobacillus_gasseri_cluster", "Sneathia_amnii", "Prevotella_cluster2", "TM7_OTU-H1")
tax_plots <- list()
tax_hists <- list()

#taxalist <- c("Lactobacillus_iners", "Lactobacillus_crispatus_cluster")
for (taxa in taxalist){
 mixed_full <- covs.taxa(full_set, taxa, "mixed", vars)
 mixed_notype <- covs.taxa(full_set, taxa, "mixed", no_type)
 print(taxa)
 print(anova(mixed_full, mixed_notype))
 #print(summary(mixed_notype))
 var = paste(taxa, "Full", sep = "_")
 var2 = paste(taxa, "NoType", sep = "_")
 tax_plots[[var]] <- agg_plot(mixed_full, taxa, full_set, mx_vars) + ggtitle(var)
 tax_plots[[var2]] <- agg_plot(mixed_notype, taxa, full_set, mx_type) + ggtitle(var2)
 tax_hists[[var]] <- make_hists(mixed_full, taxa, full_set, mx_vars) + ggtitle(var)
 tax_hists[[var2]] <- make_hists(mixed_notype, taxa, full_set, mx_type) + ggtitle(var2)
}
new_list = c("Lactobacillus_iners", "Lactobacillus_crispatus_cluster", "Gardnerella_vaginalis", "Lachnospiraceae_BVAB1", "Lactobacillus_gasseri_cluster")
perf <- data.frame()
predFrame <- data.frame()
see <- subsetFull(full_set, names(t_otu))
updated <- t_otu[,(names(t_otu) %in% names(see))]

#comb <- data.frame()
for (taxa in names(updated)){
  mixed_full <- covs.taxa(see, taxa, "mixed", vars)
  if (taxa %in% new_list){
    orig <- paste(taxa, "Orig", sep = "_")
    predicted <- paste(taxa, "Pred", sep = "_")
    pre_dat <- getData(mixed_full)
    pred <- predict(mixed_full)
    comb[1:length(pred),c(orig, predicted)] <- cbind(pre_dat[,c("tax_prop", "SUBJECT_ID")], pred)
    # comb <- comb %>%
    #   rename(!!orig := tax_prop, !!predicted := pred)
  }
  var = paste(taxa, "Full", sep = "_")
  predFrame[1:length(predict(mixed_full)),taxa] <- predict(mixed_full)
  perf[taxa,names(model_performance(mixed_full, metrics = "all", verbose = TRUE))] <- model_performance(mixed_full, metrics = "all", verbose = TRUE)
}
predFrame[predFrame < 0] <- 0
predFrame[predFrame > 1] <- 1
comb[comb < 0] <- 0
comb[comb > 1] <- 1
comb <- comb[ , c(2, 1, 3:ncol(comb))]
no_na <- na.omit(full_set[, vars])
pred_Full <- cbind(predFrame, no_na)
#Get the actual from the initial model
#Add in subject_id
#Truncate, DONE

perf$rankRMSE <- rank(perf$RMSE)
perf$rankR2Cond <- rank(-perf$R2_conditional)
perf$Name <- rownames(perf)
kable(perf,  table.attr = "style = \"color: black;\"") %>%
  kable_styling(bootstrap_options = c("striped", "hover"))

	AIC	BIC	R2_conditional	R2_marginal	ICC	RMSE	rankRMSE	rankR2Cond	Name
Acidovorax_delafieldii_temperans	-17387.410	-16959.236	0.9271641	0.2295530	0.9054628	0.0007071	8	14	Acidovorax_delafieldii_temperans
Actinobaculum_massiliense	-15720.057	-15291.883	0.1877250	0.1087328	0.0886291	0.0020474	43	112	Actinobaculum_massiliense
Actinomyces_meyeri_odontolyticus	-16192.741	-15764.567	0.2221724	0.2200070	0.0027761	0.0019171	40	107	Actinomyces_meyeri_odontolyticus
Actinomyces_oris	-17914.653	-17486.479	NA	0.2045212	NA	0.0011628	17	134	Actinomyces_oris
Actinomyces_turicensis	-17145.296	-16717.122	0.7263134	0.7259751	0.0012345	0.0014539	26	32	Actinomyces_turicensis
Actinomyces_viscosus	-23121.373	-22693.199	NA	0.9991278	NA	0.0002544	3	135	Actinomyces_viscosus
Aerococcus_christensenii	-11549.295	-11121.121	0.3151074	0.1628666	0.1818596	0.0064874	108	96	Aerococcus_christensenii
Alistipes_putredinis	-17319.223	-16891.049	0.2937339	0.0347617	0.2682988	0.0011426	16	101	Alistipes_putredinis
Alloprevotella_tannerae	-17248.765	-16820.591	0.6059447	0.6032216	0.0068629	0.0014031	24	55	Alloprevotella_tannerae
Alloscardovia_omnicolens	-19051.850	-18623.676	0.9764949	0.9704455	0.2046855	0.0007158	9	9	Alloscardovia_omnicolens
Anaerococcus_hydrogenalis	-14922.757	-14494.582	0.3844899	0.3349658	0.0744685	0.0026119	55	83	Anaerococcus_hydrogenalis
Anaerococcus_lactolyticus_cluster	-12227.660	-11799.486	0.2947407	0.1989324	0.1196008	0.0055480	98	100	Anaerococcus_lactolyticus_cluster
Anaerococcus_OTU147	-13373.748	-12945.574	0.6903183	0.6016931	0.2225047	0.0037140	77	41	Anaerococcus_OTU147
Anaerococcus_OTU153	-13596.832	-13168.658	0.0251648	0.0222535	0.0029775	0.0040891	85	132	Anaerococcus_OTU153
Anaerococcus_OTU5	-14646.079	-14217.905	0.4881823	0.4521661	0.0657429	0.0028510	57	73	Anaerococcus_OTU5
Anaerococcus_tetradius	-14025.857	-13597.683	0.2405319	0.1324379	0.1245951	0.0032709	68	106	Anaerococcus_tetradius
Anaerococcus_vaginalis	-14494.086	-14065.912	0.2064371	0.2048119	0.0020438	0.0031497	66	109	Anaerococcus_vaginalis
Anaeroglobus_geminatus	-21037.536	-20609.362	0.9351840	0.9272559	0.1089851	0.0004272	6	13	Anaeroglobus_geminatus
Arthrobacter_albus_cumminsii	-14539.968	-14111.794	0.2168729	0.1840776	0.0401941	0.0030028	61	108	Arthrobacter_albus_cumminsii
Atopobium_rimae	-15363.122	-14934.948	NA	0.0219892	NA	0.0024489	53	136	Atopobium_rimae
Atopobium_vaginae	-5190.115	-4761.940	0.7177193	0.6678172	0.1502248	0.0423779	143	38	Atopobium_vaginae
Bacteroides_cellulosilyticus_intestinalis_oleiciplenus	-19367.897	-18939.723	0.9865959	0.9864790	0.0086461	0.0007546	10	7	Bacteroides_cellulosilyticus_intestinalis_oleiciplenus
Bacteroides_coagulans	-13653.838	-13225.664	0.4043407	0.3414861	0.0954491	0.0037232	78	79	Bacteroides_coagulans
Bacteroides_fragilis	-17094.283	-16666.109	0.9927665	0.9448892	0.8687463	0.0008135	11	4	Bacteroides_fragilis
Bacteroides_massiliensis	-15873.587	-15445.413	0.3121851	0.3077049	0.0064716	0.0020969	46	97	Bacteroides_massiliensis
Bacteroides_stercoris	-14477.036	-14048.861	0.0297209	0.0267779	0.0030240	0.0031625	67	130	Bacteroides_stercoris
Bacteroides_uniformis	-16756.746	-16328.572	0.0933740	0.0891582	0.0046285	0.0016232	32	122	Bacteroides_uniformis
Bacteroides_vulgatus_dorei	-12015.922	-11587.748	0.7287686	0.7255546	0.0117110	0.0064336	107	30	Bacteroides_vulgatus_dorei
Bergeyella_sp_oral_taxon_931	-12982.393	-12554.219	0.3028418	0.0359770	0.2768241	0.0040319	84	99	Bergeyella_sp_oral_taxon_931
Bifidobacterium_bifidum	-13471.207	-13043.033	0.1020659	0.0750877	0.0291684	0.0041413	86	121	Bifidobacterium_bifidum
Bifidobacterium_breve_cluster	-11078.986	-10650.811	0.7760194	0.7646163	0.0484448	0.0081894	116	27	Bifidobacterium_breve_cluster
Bifidobacterium_dentium	-14408.210	-13980.035	0.3088783	0.0270391	0.2896716	0.0026397	56	98	Bifidobacterium_dentium
Bifidobacterium_longum_infantis_suis	-11635.179	-11207.005	0.9627866	0.9591566	0.0888780	0.0067442	112	10	Bifidobacterium_longum_infantis_suis
Bosea_cluster53	-15841.045	-15412.871	0.0337541	0.0094344	0.0245513	0.0020821	44	129	Bosea_cluster53
Bradyrhizobiaceae_cluster49	-15389.722	-14961.548	0.9070597	0.9044323	0.0274927	0.0023691	51	15	Bradyrhizobiaceae_cluster49
Brevibacterium_ravenspurgense	-16031.641	-15603.467	0.2047684	0.0859569	0.1299846	0.0018146	38	110	Brevibacterium_ravenspurgense
Campylobacter_hominis	-15670.135	-15241.961	0.7217163	0.7027838	0.0636992	0.0021178	47	36	Campylobacter_hominis
Campylobacter_ureolyticus	-10874.731	-10446.557	0.3750741	0.3215450	0.0788985	0.0084842	117	84	Campylobacter_ureolyticus
Caulobacteraceae_cluster34	-18483.008	-18054.834	0.2406715	0.2391469	0.0020038	0.0009832	13	105	Caulobacteraceae_cluster34
Clostridiaceae_1_OTU17	-14981.602	-14553.428	0.4267996	0.0927837	0.3681767	0.0021368	48	77	Clostridiaceae_1_OTU17
Clostridiales_BVAB2	-10144.740	-9716.565	0.3568899	0.1961364	0.1999760	0.0096642	119	87	Clostridiales_BVAB2
Clostridiales_BVAB3	-15805.018	-15376.844	0.5740039	0.5219274	0.1089300	0.0019677	42	62	Clostridiales_BVAB3
Clostridiales_OTU22	-11204.319	-10776.145	0.4332410	0.3862199	0.0766091	0.0077196	115	76	Clostridiales_OTU22
Clostridium_colicanis	-16601.161	-16172.987	0.5398366	0.1221161	0.4758266	0.0012553	20	63	Clostridium_colicanis
Coriobacteriaceae_OTU27	-11870.674	-11442.500	0.3226097	0.2985736	0.0342674	0.0065781	110	92	Coriobacteriaceae_OTU27
Corynebacterium_aurimucosum_nigricans	-12280.496	-11852.322	0.6031171	0.5820755	0.0503479	0.0057579	101	56	Corynebacterium_aurimucosum_nigricans
Corynebacterium_cluster45	-9984.212	-9556.037	0.6365505	0.6072596	0.0745807	0.0110394	123	49	Corynebacterium_cluster45
Corynebacterium_cluster58	-10123.409	-9695.234	0.6697698	0.6390697	0.0850582	0.0105152	122	44	Corynebacterium_cluster58
Corynebacterium_coyleae	-13420.777	-12992.603	0.2844032	0.1643998	0.1436135	0.0038522	81	102	Corynebacterium_coyleae
Corynebacterium_imitans_lipophiloflavum	-12886.473	-12458.299	0.1650645	0.1366723	0.0328869	0.0048961	92	116	Corynebacterium_imitans_lipophiloflavum
Corynebacterium_pyruviciproducens_cluster	-13655.134	-13226.960	0.5125039	0.4412694	0.1274934	0.0036374	76	68	Corynebacterium_pyruviciproducens_cluster
Corynebacterium_simulans_striatum	-16261.320	-15833.146	0.1337907	0.0947030	0.0431767	0.0018123	37	119	Corynebacterium_simulans_striatum
Corynebacterium_thomssenii_sundsvallense	-11479.381	-11051.207	0.5206713	0.3074384	0.3078901	0.0061423	105	66	Corynebacterium_thomssenii_sundsvallense
Corynebacterium_urealyticum	-17645.668	-17217.494	0.0854713	0.0692736	0.0174033	0.0012375	19	124	Corynebacterium_urealyticum
Delftia_acidovorans_lacustris_tsuruhatensis	-39739.438	-39311.264	1.0000000	1.0000000	0.6269149	0.0000013	1	1	Delftia_acidovorans_lacustris_tsuruhatensis
Dialister_cluster51	-10347.769	-9919.595	0.5386496	0.4972450	0.0823553	0.0098688	121	64	Dialister_cluster51
Dialister_invisus	-18254.521	-17826.347	0.8110256	0.7648935	0.1962178	0.0009081	12	22	Dialister_invisus
Dialister_micraerophilus	-11942.287	-11514.113	0.3590883	0.2684235	0.1239308	0.0060117	104	85	Dialister_micraerophilus
Dialister_propionicifaciens	-12741.237	-12313.063	0.4948088	0.3573199	0.2139305	0.0044904	91	71	Dialister_propionicifaciens
Dorea_longicatena	-14479.415	-14051.241	0.1611618	0.0676141	0.1003315	0.0029154	59	117	Dorea_longicatena
Enterobacteriaceae_cluster31	-8430.659	-8002.485	0.6906619	0.6890979	0.0050307	0.0184357	135	40	Enterobacteriaceae_cluster31
Enterococcus_faecalis	-15801.895	-15373.721	0.9478028	0.9461683	0.0303633	0.0020952	45	11	Enterococcus_faecalis
Ezakiella_peruensis	-13682.122	-13253.948	0.6743047	0.4525639	0.4050533	0.0030598	62	42	Ezakiella_peruensis
Faecalibacterium_prausnitzii	-19839.623	-19411.449	0.9836472	0.9834699	0.0107273	0.0006563	7	8	Faecalibacterium_prausnitzii
Fenollaria_timonensis	-15767.716	-15339.542	0.6089678	0.4477681	0.2919058	0.0017728	34	54	Fenollaria_timonensis
Finegoldia_magna	-9461.447	-9033.272	0.4884036	0.4479662	0.0732517	0.0128724	130	72	Finegoldia_magna
Fusobacterium_cluster48	-11778.202	-11350.028	0.5181079	0.4763256	0.0797868	0.0065131	109	67	Fusobacterium_cluster48
Fusobacterium_gonidiaformans_equinum	-13511.169	-13082.995	0.6135764	0.6083021	0.0134652	0.0041515	87	52	Fusobacterium_gonidiaformans_equinum
Gardnerella_vaginalis	-3526.012	-3097.837	0.7247044	0.5923336	0.3247037	0.0620045	145	33	Gardnerella_vaginalis
Gemella_morbillorum_sanguinis_haemolysans	-11713.301	-11285.127	0.3567435	0.3519466	0.0074020	0.0070561	113	88	Gemella_morbillorum_sanguinis_haemolysans
Gemella_OTU86	-12681.749	-12253.575	NA	0.6045299	NA	0.0053563	97	137	Gemella_OTU86
Haemophilus_cluster60	-12617.651	-12189.477	0.1875526	0.1609860	0.0316640	0.0053014	95	113	Haemophilus_cluster60
Helcococcus_seattlensis	-17137.023	-16708.848	NA	0.6058945	NA	0.0014591	27	138	Helcococcus_seattlensis
Lachnospiraceae_BVAB1	-3634.694	-3206.520	0.8921398	0.8758694	0.1310750	0.0676006	146	18	Lachnospiraceae_BVAB1
Lachnospiraceae_OTU33	-16458.715	-16030.541	0.3214496	0.1890243	0.1632913	0.0015665	28	93	Lachnospiraceae_OTU33
Lactobacillus_crispatus_cluster	-3036.883	-2608.709	0.9435135	0.9278223	0.2173966	0.0761257	147	12	Lactobacillus_crispatus_cluster
Lactobacillus_delbrueckii	-12241.633	-11813.459	0.9905929	0.9662504	0.7212673	0.0038535	82	5	Lactobacillus_delbrueckii
Lactobacillus_gasseri_cluster	-4971.098	-4542.924	0.8658581	0.7717616	0.4122726	0.0387450	142	20	Lactobacillus_gasseri_cluster
Lactobacillus_iners	-1813.793	-1385.619	0.8925608	0.8564098	0.2517650	0.1065701	148	17	Lactobacillus_iners
Lactobacillus_jensenii	-4259.587	-3831.413	0.7961473	0.6668447	0.3881152	0.0483247	144	24	Lactobacillus_jensenii
Megasphaera_OTU70_type1	-7467.563	-7039.389	0.3477399	0.2288477	0.1541748	0.0217420	137	89	Megasphaera_OTU70_type1
Megasphaera_OTU71_type2	-11234.891	-10806.717	0.5791815	0.5164580	0.1297169	0.0073608	114	60	Megasphaera_OTU71_type2
Metaprevotella_massiliensis	-13811.086	-13382.912	0.3464414	0.3280576	0.0273591	0.0037562	79	90	Metaprevotella_massiliensis
Moraxella_osloensis	-13329.425	-12901.251	0.0088088	0.0032703	0.0055567	0.0044102	90	133	Moraxella_osloensis
Morganella_morganii	-18406.099	-17977.925	0.9930131	0.9930050	0.0011503	0.0010063	14	3	Morganella_morganii
Moryella_indoligenes	-13804.123	-13375.949	0.3904462	0.3883232	0.0034708	0.0038472	80	82	Moryella_indoligenes
Mycoplasma_girerdii	-8433.902	-8005.727	NA	0.8597742	NA	0.0185073	136	139	Mycoplasma_girerdii
Mycoplasma_hominis	-8821.780	-8393.606	0.7451051	0.7057186	0.1338397	0.0148453	131	29	Mycoplasma_hominis
Negativicoccus_succinicivorans	-14828.361	-14400.187	0.1354207	0.1343746	0.0012086	0.0028592	58	118	Negativicoccus_succinicivorans
Neisseria_flava/mucosa/pharyngis/sicca	-16846.954	-16418.780	0.7819320	0.7803593	0.0071605	0.0015772	29	26	Neisseria_flava/mucosa/pharyngis/sicca
Neisseria_flavescens	-15206.405	-14778.231	0.0809069	0.0774925	0.0037012	0.0025544	54	126	Neisseria_flavescens
Oligella_urethralis	-13361.349	-12933.175	0.7244324	0.7211371	0.0118168	0.0043437	89	34	Oligella_urethralis
Parasutterella_excrementihominis	-21400.997	-20972.823	0.9883619	0.9880825	0.0234445	0.0004113	5	6	Parasutterella_excrementihominis
Parvimonas_OTU142	-14041.327	-13613.153	0.3307974	0.2446606	0.1140372	0.0032805	69	91	Parvimonas_OTU142
Peptoniphilus_coxii	-17929.505	-17501.330	0.3169154	0.2017410	0.1442820	0.0010327	15	94	Peptoniphilus_coxii
Peptoniphilus_duerdenii	-14219.740	-13791.566	0.6622962	0.5918521	0.1725946	0.0029932	60	45	Peptoniphilus_duerdenii
Peptoniphilus_harei	-14431.342	-14003.168	0.4231846	0.3902277	0.0540479	0.0030640	63	78	Peptoniphilus_harei
Peptoniphilus_indolicus	-13371.390	-12943.216	0.5904156	0.5097682	0.1645088	0.0038544	83	57	Peptoniphilus_indolicus
Peptoniphilus_urinimassiliensis	-16674.119	-16245.944	NA	0.6422790	NA	0.0016702	33	140	Peptoniphilus_urinimassiliensis
Peptostreptococcus_anaerobius	-15527.769	-15099.594	0.7970001	0.7961226	0.0043040	0.0023243	50	23	Peptostreptococcus_anaerobius
Porphyromonadaceae_OTU134	-13993.871	-13565.697	0.6371127	0.6003435	0.0920020	0.0033800	70	48	Porphyromonadaceae_OTU134
Porphyromonas_bennonis	-12350.176	-11922.002	0.4955297	0.4817128	0.0266589	0.0057571	100	70	Porphyromonas_bennonis
Porphyromonas_endodontalis	-17026.343	-16598.169	0.7710487	0.7568240	0.0584954	0.0014314	25	28	Porphyromonas_endodontalis
Porphyromonas_somerae	-12378.075	-11949.901	0.6273122	0.6170711	0.0267441	0.0057100	99	51	Porphyromonas_somerae
Porphyromonas_uenonis_asaccharolytica	-16090.012	-15661.838	0.8251491	0.1553773	0.7929834	0.0011826	18	21	Porphyromonas_uenonis_asaccharolytica
Prevotella_amnii	-8677.040	-8248.866	0.4499903	0.4229423	0.0468722	0.0165311	132	74	Prevotella_amnii
Prevotella_bergensis	-16186.624	-15758.450	NA	0.1950469	NA	0.0019256	41	141	Prevotella_bergensis
Prevotella_bivia	-6950.805	-6522.630	0.6510750	0.6285707	0.0605885	0.0270558	139	47	Prevotella_bivia
Prevotella_cluster2	-5822.643	-5394.469	0.7178322	0.6851120	0.1039107	0.0363862	141	37	Prevotella_cluster2
Prevotella_cluster50	-10235.123	-9806.949	0.4344745	0.2877211	0.2060336	0.0093773	118	75	Prevotella_cluster50
Prevotella_copri	-17403.038	-16974.864	NA	0.8906897	NA	0.0013501	23	142	Prevotella_copri
Prevotella_corporis	-11738.854	-11310.680	0.6731350	0.6273574	0.1228460	0.0063843	106	43	Prevotella_corporis
Prevotella_denticola	-12693.957	-12265.782	0.1223159	0.0517441	0.0744227	0.0050061	93	120	Prevotella_denticola
Prevotella_disiens	-9677.822	-9249.648	0.5740524	0.5239280	0.1052875	0.0117979	129	61	Prevotella_disiens
Prevotella_melaninogenica_cluster	-10027.073	-9598.899	0.5069715	0.4842113	0.0441269	0.0111728	126	69	Prevotella_melaninogenica_cluster
Prevotella_multiformis	-16367.291	-15939.117	0.0258672	0.0167734	0.0092490	0.0018107	36	131	Prevotella_multiformis
Prevotella_oris	-13855.232	-13427.058	0.5802765	0.5437766	0.0800044	0.0035516	72	59	Prevotella_oris
Prevotella_OTU-T3	-12322.620	-11894.446	0.1655112	0.1411768	0.0283346	0.0057950	103	115	Prevotella_OTU-T3
Prevotella_OTU44	-13504.712	-13076.538	0.3165165	0.1354243	0.2094579	0.0036033	75	95	Prevotella_OTU44
Prevotella_OTU49	-15416.529	-14988.355	0.0825019	0.0675626	0.0160218	0.0023749	52	125	Prevotella_OTU49
Prevotella_OTU54	-17478.489	-17050.315	0.0921929	0.0830236	0.0099996	0.0013082	21	123	Prevotella_OTU54
Prevotella_pleuritidis	-16390.591	-15962.417	0.1967202	0.1876299	0.0111898	0.0017952	35	111	Prevotella_pleuritidis
Prevotellaceae_OTU61	-13630.966	-13202.792	0.2570843	0.1103191	0.1649638	0.0035721	74	104	Prevotellaceae_OTU61
Propionibacterium_acnes	-12343.547	-11915.373	0.7890623	0.7835592	0.0254255	0.0057745	102	25	Propionibacterium_acnes
Propionibacterium_avidum_propionicum	-22634.687	-22206.513	0.5900243	0.5700952	0.0463571	0.0002813	4	58	Propionibacterium_avidum_propionicum
Propionimicrobium_lymphophilum	-15415.931	-14987.757	0.3580599	0.2975746	0.0861092	0.0022417	49	86	Propionimicrobium_lymphophilum
Proteobacteria_OTU-T1	-11803.483	-11375.309	0.3916603	0.0059571	0.3880146	0.0053444	96	81	Proteobacteria_OTU-T1
Pseudomonas_aeruginosa	-28946.442	-28518.268	0.9994494	0.9994403	0.0161400	0.0000458	2	2	Pseudomonas_aeruginosa
Pseudomonas_gessardii_cluster	-10051.331	-9623.157	NA	0.7282996	NA	0.0115428	128	143	Pseudomonas_gessardii_cluster
Pyramidobacter_sp	-17463.554	-17035.380	NA	0.1746499	NA	0.0013265	22	144	Pyramidobacter_sp
Rothia_mucilaginosa	-14543.629	-14115.455	0.3920836	0.3891579	0.0047896	0.0030964	64	80	Rothia_mucilaginosa
Shuttleworthia_satelles	-16847.007	-16418.833	NA	0.0235293	NA	0.0015880	30	145	Shuttleworthia_satelles
Sneathia_amnii	-6506.739	-6078.565	0.6302520	0.5494910	0.1792661	0.0283143	140	50	Sneathia_amnii
Sneathia_OTU65	-15287.130	-14858.956	0.7278586	0.0364789	0.7175554	0.0015885	31	31	Sneathia_OTU65
Sneathia_sanguinegens	-9242.268	-8814.094	0.6103573	0.3267148	0.4212813	0.0110825	124	53	Sneathia_sanguinegens
Staphylococcus_cluster47	-9972.464	-9544.290	0.9052482	0.9025158	0.0280285	0.0115103	127	16	Staphylococcus_cluster47
Stenotrophomonas_rhizophila	-14132.455	-13704.281	0.2580453	0.2554337	0.0035075	0.0034955	71	103	Stenotrophomonas_rhizophila
Streptococcus_agalactiae	-9996.456	-9568.282	0.8911707	0.8841266	0.0607908	0.0111201	125	19	Streptococcus_agalactiae
Streptococcus_anginosus	-10201.064	-9772.889	0.7218227	0.6671497	0.1642571	0.0097254	120	35	Streptococcus_anginosus
Streptococcus_cluster29	-7157.037	-6728.863	NA	0.7616446	NA	0.0268661	138	146	Streptococcus_cluster29
Streptococcus_parasanguinis	-14245.346	-13817.172	0.1813025	0.0935078	0.0968511	0.0031295	65	114	Streptococcus_parasanguinis
Streptococcus_salivarius_thermophilus_vestibularis	-12741.409	-12313.235	NA	0.2848975	NA	0.0052639	94	147	Streptococcus_salivarius_thermophilus_vestibularis
Sutterella_sanguinis	-16261.200	-15833.026	0.0779703	0.0603826	0.0187179	0.0018514	39	127	Sutterella_sanguinis
TM7_OTU-H1	-8029.654	-7601.480	0.5272706	0.4295954	0.1712384	0.0182472	134	65	TM7_OTU-H1
Ureaplasma_cluster23	-8382.795	-7954.621	0.7026208	0.6466340	0.1584385	0.0165980	133	39	Ureaplasma_cluster23
Veillonella_cluster61	-11907.828	-11479.654	NA	0.2620593	NA	0.0067139	111	148	Veillonella_cluster61
Veillonella_montpellierensis	-14048.875	-13620.701	0.0577799	0.0511873	0.0069483	0.0035701	73	128	Veillonella_montpellierensis
Weeksella_virosa	-13505.758	-13077.583	0.6554187	0.6517386	0.0105671	0.0041692	88	46	Weeksella_virosa

#make boxplot for the metrics and look at outliers, use rmse
#see rank of metrics for specific taxa of interest
#add column for quantiles for the specific taxa of interest
rmse <- ggplot(perf, aes(x="RMSE", y=RMSE)) + 
  geom_boxplot() +
  geom_point(data=subset(perf, rownames(perf) %in% new_list), 
    aes(x="RMSE", y=RMSE), 
    color="red", size=5) +
  geom_text_repel(data=subset(perf, rownames(perf) %in% new_list), aes(label=Name))
rmse

r2_cond <- ggplot(perf, aes(x="R2_Cond", y=R2_conditional)) + 
  geom_boxplot() +
  geom_point(data=subset(perf, rownames(perf) %in% new_list), 
    aes(x="R2_Cond", y=R2_conditional), 
    color="red", size=5) +
  geom_text_repel(data=subset(perf, rownames(perf) %in% new_list), aes(label=Name))
r2_cond

marrangeGrob(tax_plots, nrow = 2, ncol = 2)

marrangeGrob(tax_hists, nrow = 2, ncol = 2)

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

iners_f_hist <- make_hists(iners_fixed, "Lactobacillus_iners", full_set, vars) + ggtitle("Iners Fixed Plot")
iners_m_hist <- make_hists(iners_mixed, "Lactobacillus_iners", full_set, mx_vars) + ggtitle("Iners Mixed Plot")
ggarrange(iners_f_hist, iners_m_hist)

crisp_f_hist <- make_hists(crisp_fixed, "Lactobacillus_crispatus_cluster", full_set, vars) + ggtitle("Crisp Fixed Plot")
crisp_m_hist <- make_hists(crisp_mixed, "Lactobacillus_crispatus_cluster", full_set, mx_vars) + ggtitle("Crisp Mixed Plot")
ggarrange(crisp_f_hist, crisp_m_hist)

#clean age, set blanks to NA, clean values, make 18-28 reference group
# do individual plots
# quantify prediction success
# get model summaries
# perform on more taxa
#education, high_school_ged is baseline, put in order of ascending degree

#predictions <- pred_plot(full_set, mod_Iners)
#lapply(models, model_plot)

mod_Crisp <- taxa.glm(full_set, "Lactobacillus_crispatus_cluster", "class", "fixed")
mod_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "class", "fixed")
mod_BVAB <- taxa.glm(full_set, "Lachnospiraceae_BVAB1", "class", "fixed")
mod_Gard <- taxa.glm(full_set, "Gardnerella_vaginalis", "class", "fixed")
mod_Gass <- taxa.glm(full_set, "Lactobacillus_gasseri_cluster", "class", "fixed")

prop_Crisp <- taxa.glm(full_set, "Lactobacillus_crispatus_cluster", "prop", "fixed")
prop_Iners <- taxa.glm(full_set, "Lactobacillus_iners", "prop", "fixed")
prop_BVAB <- taxa.glm(full_set, "Lachnospiraceae_BVAB1", "prop", "fixed")
prop_Gard <- taxa.glm(full_set, "Gardnerella_vaginalis", "prop", "fixed")
prop_Gass <- taxa.glm(full_set, "Lactobacillus_gasseri_cluster", "prop", "fixed")

ggarrange(model_plot(mod_Crisp), model_plot(prop_Crisp),labels = c("Class Crisp", "Prop Crisp"))
ggarrange(model_plot(mod_Iners), model_plot(prop_Iners),labels = c("Class Iners", "Prop Iners"))
ggarrange(model_plot(mod_BVAB), model_plot(prop_BVAB),labels = c("Class BVAB", "Prop BVAB"))
ggarrange(model_plot(mod_Crisp), model_plot(prop_Iners),labels = c("Class Gard", "Prop Gard"))
ggarrange(model_plot(mod_Gass), model_plot(prop_Gass),labels = c("Class Gass", "Prop Gass"))
model_plot(mod_Crisp) + ggtitle("Class Crispatus")
model_plot(mod_Iners) + ggtitle("Class Iners")
model_plot(mod_BVAB) + ggtitle("Class BVAB")
model_plot(mod_Gard) + ggtitle("Class Gardnerella")
model_plot(mod_Gass) + ggtitle("Class Gasseri")

#alpha_div and vagitype show up in almost every model vaginal_pH in most of them
#correlations between data
#longitudinal plots when stratifying by covariates
#count and proportion plots
#Look at model pre and post aic
#ggaly and regular correlation matrix
#Look at distribution of NA's in covariate (pre-filtering) and see if it affects model by removing it

mixed_Iners <- taxa.glm(full_set, "Lactobacillus_crispatus_cluster", "mean", "mixed")
#Some linear combination of the parameters perfectly separates failure from successes, I assume it's vagitype
#Doesn't run still

na.test <-  function (x) {
  w <- sapply(x, function(x)all(is.na(x)))
  if (any(w)) {
    stop(paste("All NA in columns", paste(which(w), collapse=", ")))
  }
}
#Recode High to 1 and Low to 0
full_set[["class_Iners"]] <- recode(full_set[["class_Iners"]], "High"= 1, "Low"= 0)
full_set$class_Iners <- as.factor(full_set$class_Iners)


covs <- c("class_Iners", "vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "income", "bv", "phys", "antibiotics_current","SUBJECT_ID")
model_data <- full_set[,covs]
no.na.data <- na.omit(model_data)

reduced_mod <- glmer(class_Iners ~ alpha_div + vagitype + (1|SUBJECT_ID), data = no.na.data, family = binomial, control=glmerControl(optimizer="bobyqa",optCtrl=list(maxfun=2e5))) #Unable to evaluate scaled gradient, model fails to converge
step.model <- stepAIC(log_mod, direction = "both", 
                      trace = FALSE)
#install.packages("ResourceSelection")
library(ResourceSelection)

fixed_mod <- glm(class_Iners ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + phys + bv + antibiotics_current, data = no.na.data, family = binomial) 
step.model <- stepAIC(fixed_mod, direction = "both", 
                      trace = FALSE)
step.back <- stepAIC(fixed_mod, direction = "backward")
hoslem.test(no.na.data$class_Iners, fitted(fixed_mod))
hoslem.test(no.na.data$class_Iners, fitted(step.model))
# model becomes class_Iners ~ alpha_div + vagitype
predict(fixed_mod, type = "response")
histogram(predict(fixed_mod, type = "response"))
plot(predict(fixed_mod, type = "response"), full_set$class_Iners)



plotting_dfm <- expand.grid(alpha_div = seq(0, 3.5, 0.01),
                           vagitype = c("Lactobacillus_crispatus_cluster", "Lactobacillus_iners", "Lachnospiraceae_BVAB1", "Gardnerella_vaginalis", "Lactobacillus_gasseri_cluster"))
plotting_dfm$preds <- predict(step.model, newdata=plotting_dfm, type = "response")
pl <- ggplot(plotting_dfm, aes(x=alpha_div, y =preds, color=as.factor(vagitype)))
pl + 
  geom_point( ) +
  ggtitle("Predicted High/Low by Alpha_Div and Vagitype")

#Look at alpha div and vagitype over trimesters and see how it changes 
# plot those who change
#Table of amt that change vs not change

reduced_mod <- glmer(class_Crisp ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + (1|SUBJECT_ID), data = full_set, family = binomial) #Does not converge
reduced_mod <- glmer(class_Gass ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + (1|SUBJECT_ID), data = full_set, family = binomial) #Does not converge
reduced_mod <- glmer(class_Gard ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + (1|SUBJECT_ID), data = full_set, family = binomial) #Does not converge
reduced_mod <- glmer(class_BVAB ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + (1|SUBJECT_ID), data = full_set, family = binomial) #Does not converge

library(caret)

#Split Data 80:20
training.samps <- full_set$class_Iners %>%
  createDataPartition(p = 0.8, list = FALSE)
train.data <- full_set[training.samps,]
test.data <- full_set[-training.samps,]
#Linear discriminant analysis
#install.packages("mda")
library(mda)
covs_test <- as.data.frame(test.data[,cov])
full_set$vagitype <- as.factor(full_set$vagitype)
full_set$SUBJECT_ID <- as.factor(full_set$SUBJECT_ID)
mda_model <- mda(class_Iners ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + SUBJECT_ID, data = full_set)
#summary(mda_model)
mda_model$percent.explained
mda_model$confusion
covs <- covs[which(names(pred) %in% rownames(full_set)),]
#mda_pred <- predict(mda_model,test.data)


# SVM
library(e1071)
rownames(full_set) <- rownames(meta)
cov <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "income", "SUBJECT_ID")
covs <- as.data.frame(full_set[,cov])
svm_model <- svm(class_Iners ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + income + SUBJECT_ID, data = full_set, type = "C")
pred <- predict(svm_model, covs)
table(pred, full_set$class_Iners[which(names(pred) %in% rownames(full_set))])
#Random Forest
#try randomforest with formula and see if random var works
#install.packages("randomForest")
#library(randomForest)
#full_set$vagitype <- as.character(full_set$vagitype)
#full_set$SUBJECT_ID <- as.character(full_set$SUBJECT_ID)
#forest_model <- randomForest(class_Iners ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = full_set, na.action=na.omit, importance = TRUE)

#Split Data 80:20
training.samps <- full_set$class_Snea %>%
  createDataPartition(p = 0.8, list = FALSE)
train.data <- full_set[training.samps,]
test.data <- full_set[-training.samps,]
#Linear discriminant analysis
#install.packages("mda")
library(mda)
covs_test <- as.data.frame(test.data[,cov])
full_set$vagitype <- as.factor(full_set$vagitype)
full_set$SUBJECT_ID <- as.factor(full_set$SUBJECT_ID)
mda_model <- mda(class_Snea ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = train.data)
#summary(mda_model)
mda_model$percent.explained
mda_model$confusion
covs <- covs[which(names(pred) %in% rownames(full_set)),]
#mda_pred <- predict(mda_model,test.data)


# SVM
library(e1071)
rownames(full_set) <- rownames(meta)
cov <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "SUBJECT_ID")
covs <- as.data.frame(full_set[,cov])
svm_model <- svm(class_Snea ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = full_set, type = "C")
pred <- predict(svm_model, covs)
table(pred, full_set$class_Snea[which(names(pred) %in% rownames(full_set))])

#Split Data 80:20
training.samps <- full_set$class_Prev %>%
  createDataPartition(p = 0.8, list = FALSE)
train.data <- full_set[training.samps,]
test.data <- full_set[-training.samps,]
#Linear discriminant analysis
#install.packages("mda")
library(mda)
covs_test <- as.data.frame(test.data[,cov])
full_set$vagitype <- as.factor(full_set$vagitype)
full_set$SUBJECT_ID <- as.factor(full_set$SUBJECT_ID)
mda_model <- mda(class_Prev ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = train.data)
#summary(mda_model)
mda_model$percent.explained
covs <- covs[which(names(pred) %in% rownames(full_set)),]
mda_model$confusion

#mda_pred <- predict(mda_model,test.data)


# SVM
library(e1071)
rownames(full_set) <- rownames(meta)
cov <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "SUBJECT_ID")
covs <- as.data.frame(full_set[,cov])
svm_model <- svm(class_Prev ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = full_set, type = "C")
pred <- predict(svm_model, covs)
table(pred, full_set$class_Prev[which(names(pred) %in% rownames(full_set))])

#Split Data 80:20
training.samps <- full_set$class_TM %>%
  createDataPartition(p = 0.8, list = FALSE)
train.data <- full_set[training.samps,]
test.data <- full_set[-training.samps,]
#Linear discriminant analysis
#install.packages("mda")
library(mda)
covs_test <- as.data.frame(test.data[,cov])
full_set$vagitype <- as.factor(full_set$vagitype)
full_set$SUBJECT_ID <- as.factor(full_set$SUBJECT_ID)
mda_model <- mda(class_TM ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = train.data)
#summary(mda_model)
mda_model$percent.explained
covs <- covs[which(names(pred) %in% rownames(full_set)),]
mda_model$confusion
#mda_pred <- predict(mda_model,test.data)


# SVM
library(e1071)
rownames(full_set) <- rownames(meta)
cov <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "SUBJECT_ID")
covs <- as.data.frame(full_set[,cov])
svm_model <- svm(class_TM ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = full_set, type = "C")
pred <- predict(svm_model, covs)
table(pred, full_set$class_TM[which(names(pred) %in% rownames(full_set))])

#Split Data 80:20
training.samps <- full_set$class_BVAB %>%
  createDataPartition(p = 0.8, list = FALSE)
train.data <- full_set[training.samps,]
test.data <- full_set[-training.samps,]
#Linear discriminant analysis
#install.packages("mda")
library(mda)
covs_test <- as.data.frame(test.data[,cov])
full_set$vagitype <- as.factor(full_set$vagitype)
full_set$SUBJECT_ID <- as.factor(full_set$SUBJECT_ID)
mda_model <- mda(class_BVAB ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = train.data)
#summary(mda_model)
mda_model$percent.explained
covs <- covs[which(names(pred) %in% rownames(full_set)),]
mda_model$confusion
#mda_pred <- predict(mda_model,test.data)


# SVM
library(e1071)
rownames(full_set) <- rownames(meta)
cov <- c("vaginal_pH", "reported_ga", "alpha_div", "race", "vagitype", "SUBJECT_ID")
covs <- as.data.frame(full_set[,cov])
svm_model <- svm(class_BVAB ~ vaginal_pH + reported_ga + alpha_div + race + vagitype + SUBJECT_ID, data = full_set, type = "C")
pred <- predict(svm_model, covs)
table(pred, full_set$class_BVAB[which(names(pred) %in% rownames(full_set))])